NCBI Taxonomy: a comprehensive update on curation, resources and tools

CL Schoch, S Ciufo, M Domrachev, CL Hotton… - Database, 2020 - academic.oup.com
Abstract The National Center for Biotechnology Information (NCBI) Taxonomy includes
organism names and classifications for every sequence in the nucleotide and protein …

Fungal identification using molecular tools: a primer for the natural products research community

HA Raja, AN Miller, CJ Pearce… - Journal of natural …, 2017 - ACS Publications
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They
are known to produce numerous bioactive molecules, which makes them very useful for …

Action mechanisms and research methods of tRNA-derived small RNAs

Y Xie, L Yao, X Yu, Y Ruan, Z Li, J Guo - Signal transduction and …, 2020 - nature.com
Abstract tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and
tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or …

FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild

NH Nguyen, Z Song, ST Bates, S Branco, L Tedersoo… - Fungal ecology, 2016 - Elsevier
Fungi typically live in highly diverse communities composed of multiple ecological guilds.
Although high-throughput sequencing has greatly increased the ability to quantify the …

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

LM van der Loos, R Nijland - Molecular Ecology, 2021 - Wiley Online Library
With the growing anthropogenic pressure on marine ecosystems, the need for efficient
monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is …

Towards a unified paradigm for sequence‐based identification of fungi

U Kõljalg, RH Nilsson, K Abarenkov, L Tedersoo… - 2013 - Wiley Online Library
The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode
and in most cases the marker of choice for the exploration of fungal diversity in …

Assessment of BOLD and GenBank–Their accuracy and reliability for the identification of biological materials

KA Meiklejohn, N Damaso, JM Robertson - PloS one, 2019 - journals.plos.org
Taxonomic identification of biological materials can be achieved through DNA barcoding,
where an unknown “barcode” sequence is compared to a reference database. In many …

DNA Sequence-Based Identification of Fusarium: A Work in Progress

K O'Donnell, BK Whitaker, I Laraba, RH Proctor… - Plant …, 2022 - Am Phytopath Society
Accurate species-level identification of an etiological agent is crucial for disease diagnosis
and management because knowing the agent's identity connects it with what is known about …

Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis

TM Porter, M Hajibabaei - Molecular ecology, 2018 - Wiley Online Library
The purpose of this review is to present the most common and emerging DNA‐based
methods used to generate data for biodiversity and biomonitoring studies. As environmental …

DNA sequence-based identification of Fusarium: Current status and future directions

K O'Donnell, TJ Ward, VARG Robert, PW Crous… - Phytoparasitica, 2015 - Springer
Fusarium ranks as one of the world's most economically destructive and species-rich groups
of mycotoxigenic plant pathogens (Aoki et al. 2014). These ubiquitous molds produce a …